Run each subcommand and ensure proper behavior

[lavanyarishishwar]

Following set of commands perform the full run:

!/bin/bash

threads=30

step 1: build a haplotype file

echo "#########################################################" echo "Running step 1" ./pastrami.py hapmake --map-dir map_data --haplotypes african.hap -v echo "#########################################################"

echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" echo "Running step 2"

step 2: build database (pickle file)

./pastrami.py build --reference-pickle african.pickle --reference-prefix maskedAfricanChrAllReference --haplotype african.hap -v --threads $threads echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"

echo "*****" echo "Running step 3"

step 3: querying the database

./pastrami.py query --reference-pickle african.pickle --query-prefix maskedAfricanChrAllQuery --combined-out african.tsv --query-out african_query.tsv -v --threads $threads echo "*****"

echo "---------------------------------------------------------" echo "Running step 4"

step 4: aggregate the results

cat maskedAfricanChrAllQuery.tfam maskedAfricanChrAllReference.tfam > input.tfam ./pastrami.py aggregate --pop-group pop2group.txt --pastrami-output african.tsv --pastrami-fam input.tfam -v --threads $threads echo "---------------------------------------------------------"

[lavanyarishishwar]

• Run started at: 02-20-2021 08:20:13 PM
• Run successfully finished at: 02-20-2021 09:13:29 PM